Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2589205199', 'doi': 'https://doi.org/10.1093/bioinformatics/btx101', 'title': 'BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank', 'display_name': 'BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank', 'publication_year': 2017, 'publication_date': '2017-02-16', 'ids': {'openalex': 'https://openalex.org/W2589205199', 'doi': 'https://doi.org/10.1093/bioinformatics/btx101', 'mag': '2589205199', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/28334105', 'pmcid': 'https://www.ncbi.nlm.nih.gov/pmc/articles/5870676'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btx101', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'hybrid', 'oa_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.pdf', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5014978419', 'display_name': 'Jianjiong Gao', 'orcid': 'https://orcid.org/0000-0002-5739-1781'}, 'institutions': [{'id': 'https://openalex.org/I76835614', 'display_name': 'University of Missouri', 'ror': 'https://ror.org/02ymw8z06', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I76835614']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Jianjiong Gao', 'raw_affiliation_strings': ['Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA'], 'affiliations': [{'raw_affiliation_string': 'Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA', 'institution_ids': ['https://openalex.org/I76835614']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5077634829', 'display_name': 'Andreas Prlić', 'orcid': 'https://orcid.org/0000-0001-6346-6391'}, 'institutions': [{'id': 'https://openalex.org/I36258959', 'display_name': 'University of California, San Diego', 'ror': 'https://ror.org/0168r3w48', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I36258959']}, {'id': 'https://openalex.org/I181653535', 'display_name': 'San Diego Supercomputer Center', 'ror': 'https://ror.org/04mg3nk07', 'country_code': 'US', 'type': 'facility', 'lineage': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Andreas Prlić', 'raw_affiliation_strings': ['RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA'], 'affiliations': [{'raw_affiliation_string': 'RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA', 'institution_ids': ['https://openalex.org/I36258959', 'https://openalex.org/I181653535']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5037719857', 'display_name': 'Chunxiao Bi', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I181653535', 'display_name': 'San Diego Supercomputer Center', 'ror': 'https://ror.org/04mg3nk07', 'country_code': 'US', 'type': 'facility', 'lineage': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}, {'id': 'https://openalex.org/I36258959', 'display_name': 'University of California, San Diego', 'ror': 'https://ror.org/0168r3w48', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I36258959']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Chunxiao Bi', 'raw_affiliation_strings': ['RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA'], 'affiliations': [{'raw_affiliation_string': 'RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA', 'institution_ids': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5053815083', 'display_name': 'Wolfgang F. Bluhm', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I181653535', 'display_name': 'San Diego Supercomputer Center', 'ror': 'https://ror.org/04mg3nk07', 'country_code': 'US', 'type': 'facility', 'lineage': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}, {'id': 'https://openalex.org/I36258959', 'display_name': 'University of California, San Diego', 'ror': 'https://ror.org/0168r3w48', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I36258959']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Wolfgang F Bluhm', 'raw_affiliation_strings': ['RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA'], 'affiliations': [{'raw_affiliation_string': 'RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA', 'institution_ids': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5074348793', 'display_name': 'Dimitris Dimitropoulos', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I181653535', 'display_name': 'San Diego Supercomputer Center', 'ror': 'https://ror.org/04mg3nk07', 'country_code': 'US', 'type': 'facility', 'lineage': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}, {'id': 'https://openalex.org/I36258959', 'display_name': 'University of California, San Diego', 'ror': 'https://ror.org/0168r3w48', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I36258959']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Dimitris Dimitropoulos', 'raw_affiliation_strings': ['RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA'], 'affiliations': [{'raw_affiliation_string': 'RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA', 'institution_ids': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5082428303', 'display_name': 'Dong Xu', 'orcid': 'https://orcid.org/0000-0002-4809-0514'}, 'institutions': [{'id': 'https://openalex.org/I76835614', 'display_name': 'University of Missouri', 'ror': 'https://ror.org/02ymw8z06', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I76835614']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Dong Xu', 'raw_affiliation_strings': ['Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA'], 'affiliations': [{'raw_affiliation_string': 'Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA', 'institution_ids': ['https://openalex.org/I76835614']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5075833022', 'display_name': 'Philip E. Bourne', 'orcid': 'https://orcid.org/0000-0002-7618-7292'}, 'institutions': [{'id': 'https://openalex.org/I36258959', 'display_name': 'University of California, San Diego', 'ror': 'https://ror.org/0168r3w48', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I36258959']}, {'id': 'https://openalex.org/I181653535', 'display_name': 'San Diego Supercomputer Center', 'ror': 'https://ror.org/04mg3nk07', 'country_code': 'US', 'type': 'facility', 'lineage': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Philip E Bourne', 'raw_affiliation_strings': ['RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA', 'Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA'], 'affiliations': [{'raw_affiliation_string': 'Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA', 'institution_ids': ['https://openalex.org/I36258959']}, {'raw_affiliation_string': 'RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA', 'institution_ids': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5070583038', 'display_name': 'Peter W. Rose', 'orcid': 'https://orcid.org/0000-0001-9981-9750'}, 'institutions': [{'id': 'https://openalex.org/I181653535', 'display_name': 'San Diego Supercomputer Center', 'ror': 'https://ror.org/04mg3nk07', 'country_code': 'US', 'type': 'facility', 'lineage': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}, {'id': 'https://openalex.org/I36258959', 'display_name': 'University of California, San Diego', 'ror': 'https://ror.org/0168r3w48', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I36258959']}], 'countries': ['US'], 'is_corresponding': True, 'raw_author_name': 'Peter W Rose', 'raw_affiliation_strings': ['RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA'], 'affiliations': [{'raw_affiliation_string': 'RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA', 'institution_ids': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959']}]}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 3, 'corresponding_author_ids': ['https://openalex.org/A5070583038'], 'corresponding_institution_ids': ['https://openalex.org/I181653535', 'https://openalex.org/I36258959'], 'apc_list': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'apc_paid': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'fwci': 0.798, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 10, 'citation_normalized_percentile': {'value': 0.501791, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 85, 'max': 86}, 'biblio': {'volume': '33', 'issue': '13', 'first_page': '2047', 'last_page': '2049'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T11162', 'display_name': 'Enzyme Structure and Function', 'score': 0.9994, 'subfield': {'id': 'https://openalex.org/subfields/2505', 'display_name': 'Materials Chemistry'}, 'field': {'id': 'https://openalex.org/fields/25', 'display_name': 'Materials Science'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, 'topics': [{'id': 'https://openalex.org/T11162', 'display_name': 'Enzyme Structure and Function', 'score': 0.9994, 'subfield': {'id': 'https://openalex.org/subfields/2505', 'display_name': 'Materials Chemistry'}, 'field': {'id': 'https://openalex.org/fields/25', 'display_name': 'Materials Science'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, {'id': 'https://openalex.org/T10044', 'display_name': 'Protein Structure and Dynamics', 'score': 0.9991, 'subfield': {'id': 'https://openalex.org/subfields/1312', 'display_name': 'Molecular Biology'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, {'id': 'https://openalex.org/T10519', 'display_name': 'Advanced Proteomics Techniques and Applications', 'score': 0.9951, 'subfield': {'id': 'https://openalex.org/subfields/1607', 'display_name': 'Spectroscopy'}, 'field': {'id': 'https://openalex.org/fields/16', 'display_name': 'Chemistry'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}], 'keywords': [{'id': 'https://openalex.org/keywords/protein-data-bank', 'display_name': 'Protein Data Bank', 'score': 0.9244584}, {'id': 'https://openalex.org/keywords/mit-license', 'display_name': 'MIT License', 'score': 0.81607294}], 'concepts': [{'id': 'https://openalex.org/C65556437', 'wikidata': 'https://www.wikidata.org/wiki/Q766195', 'display_name': 'Protein Data Bank (RCSB PDB)', 'level': 2, 'score': 0.9829593}, {'id': 'https://openalex.org/C119145174', 'wikidata': 'https://www.wikidata.org/wiki/Q7251429', 'display_name': 'Protein Data Bank', 'level': 3, 'score': 0.9244584}, {'id': 'https://openalex.org/C174183944', 'wikidata': 'https://www.wikidata.org/wiki/Q334661', 'display_name': 'MIT License', 'level': 3, 'score': 0.81607294}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.5627379}, {'id': 'https://openalex.org/C2777904410', 'wikidata': 'https://www.wikidata.org/wiki/Q7397', 'display_name': 'Software', 'level': 2, 'score': 0.44194135}, {'id': 'https://openalex.org/C47701112', 'wikidata': 'https://www.wikidata.org/wiki/Q735188', 'display_name': 'Protein structure', 'level': 2, 'score': 0.4151042}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.32799426}, {'id': 'https://openalex.org/C77088390', 'wikidata': 'https://www.wikidata.org/wiki/Q8513', 'display_name': 'Database', 'level': 1, 'score': 0.32132316}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.26016912}, {'id': 'https://openalex.org/C199360897', 'wikidata': 'https://www.wikidata.org/wiki/Q9143', 'display_name': 'Programming language', 'level': 1, 'score': 0.10925853}, {'id': 'https://openalex.org/C55493867', 'wikidata': 'https://www.wikidata.org/wiki/Q7094', 'display_name': 'Biochemistry', 'level': 1, 'score': 0.08939916}], 'mesh': [{'descriptor_ui': 'D019295', 'descriptor_name': 'Computational Biology', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D030562', 'descriptor_name': 'Databases, Protein', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D011487', 'descriptor_name': 'Protein Conformation', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D012984', 'descriptor_name': 'Software', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D019295', 'descriptor_name': 'Computational Biology', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D020407', 'descriptor_name': 'Internet', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 5, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btx101', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://europepmc.org/articles/pmc5870676', 'pdf_url': 'https://europepmc.org/articles/pmc5870676?pdf=render', 'source': {'id': 'https://openalex.org/S4306400806', 'display_name': 'Europe PMC (PubMed Central)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1303153112', 'host_organization_name': 'European Bioinformatics Institute', 'host_organization_lineage': ['https://openalex.org/I1303153112'], 'host_organization_lineage_names': ['European Bioinformatics Institute'], 'type': 'repository'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://escholarship.org/uc/item/3594r4hm', 'pdf_url': 'https://escholarship.org/content/qt3594r4hm/qt3594r4hm.pdf?t=s0zn1o', 'source': {'id': 'https://openalex.org/S4306400115', 'display_name': 'eScholarship (California Digital Library)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I2801248553', 'host_organization_name': 'California Digital Library', 'host_organization_lineage': ['https://openalex.org/I2801248553'], 'host_organization_lineage_names': ['California Digital Library'], 'type': 'repository'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870676', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S2764455111', 'display_name': 'PubMed Central', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/28334105', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306525036', 'display_name': 'PubMed', 'issn_l': None, 'issn': None, 'is_oa': False, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}], 'best_oa_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btx101', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [{'score': 0.49, 'display_name': 'Partnerships for the goals', 'id': 'https://metadata.un.org/sdg/17'}], 'grants': [{'funder': 'https://openalex.org/F4320306076', 'funder_display_name': 'National Science Foundation', 'award_id': 'NSF DBI DBI-1338415'}, {'funder': 'https://openalex.org/F4320306076', 'funder_display_name': 'National Science Foundation', 'award_id': 'NSF DBI-0829586'}, {'funder': 'https://openalex.org/F4320332161', 'funder_display_name': 'National Institutes of Health', 'award_id': 'R01-GM100701'}, {'funder': 'https://openalex.org/F4320332161', 'funder_display_name': 'National Institutes of Health', 'award_id': 'R33-GM078601'}], 'datasets': [], 'versions': [], 'referenced_works_count': 8, 'referenced_works': ['https://openalex.org/W1975681329', 'https://openalex.org/W1989962769', 'https://openalex.org/W1999615477', 'https://openalex.org/W2021177388', 'https://openalex.org/W2105803236', 'https://openalex.org/W2130479394', 'https://openalex.org/W2157122545', 'https://openalex.org/W2170441710'], 'related_works': ['https://openalex.org/W4353055924', 'https://openalex.org/W3126783617', 'https://openalex.org/W3093468851', 'https://openalex.org/W2952811294', 'https://openalex.org/W2806488847', 'https://openalex.org/W2772651271', 'https://openalex.org/W2732388178', 'https://openalex.org/W2589205199', 'https://openalex.org/W2134815007', 'https://openalex.org/W2121688928'], 'abstract_inverted_index': {'Abstract': [0], 'Summary': [1], 'We': [2, 44, 57, 71], 'developed': [3, 59], 'a': [4, 60], 'new': [5], 'software': [6], 'tool,': [7], 'BioJava-ModFinder,': [8, 103], 'for': [9], 'identifying': [10], 'protein': [11, 31, 69, 84, 112], 'modifications': [12, 32, 47, 66], 'observed': [13], 'in': [14, 18, 39, 67, 99], '3D': [15, 68, 97], 'structures': [16, 98, 110], 'archived': [17], 'the': [19, 77, 88, 100, 122], 'Protein': [20], 'Data': [21], 'Bank': [22], '(PDB).': [23], 'Information': [24], 'on': [25, 121], 'more': [26, 106], 'than': [27, 107], '400': [28], 'types': [29], 'of': [30], 'were': [33], 'collected': [34], 'and': [35, 42, 55, 82, 91, 119, 127], 'curated': [36], 'from': [37], 'annotations': [38, 86], 'PDB,': [40], 'RESID,': [41], 'PSI-MOD.': [43], 'divided': [45], 'these': [46, 65], 'into': [48], 'three': [49], 'categories:': [50], 'modified': [51], 'residues,': [52], 'attachment': [53], 'modifications,': [54, 113], 'cross-links.': [56], 'have': [58, 72], 'systematic': [61], 'method': [62], 'to': [63, 87], 'identify': [64], 'structures.': [70], 'integrated': [73], 'this': [74], 'package': [75], 'with': [76, 111], 'RCSB': [78, 123, 140], 'PDB': [79, 101, 124, 141], 'web': [80], 'application': [81], 'added': [83], 'modification': [85], 'sequence': [89], 'diagram': [90], 'structure': [92], 'display.': [93], 'By': [94], 'scanning': [95], 'all': [96], 'using': [102], 'we': [104], 'identified': [105], '30': [108], '000': [109], 'which': [114], 'can': [115, 142], 'be': [116, 143], 'searched,': [117], 'browsed,': [118], 'visualized': [120], 'website.': [125], 'Availability': [126], 'Implementation': [128], 'BioJava-ModFinder': [129], 'is': [130], 'available': [131], 'as': [132], 'open': [133], 'source': [134], '(LGPL': [135], 'license)': [136], 'at': [137, 145], '(https://github.com/biojava/biojava/tree/master/biojava-modfinder).': [138], 'The': [139], 'accessed': [144], 'http://www.rcsb.org.': [146]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2589205199', 'counts_by_year': [{'year': 2024, 'cited_by_count': 1}, {'year': 2020, 'cited_by_count': 2}, {'year': 2019, 'cited_by_count': 5}, {'year': 2018, 'cited_by_count': 1}, {'year': 2016, 'cited_by_count': 1}], 'updated_date': '2024-12-24T11:43:25.937209', 'created_date': '2017-03-03'}